Error occurred performing CAIC

[Jiani Yin]

Hi,

I am trying to use CAIC to normalize raw Hi-C matrices (100kb bins). The raw matrices were generated using HiC-Pro_2.11.1, python 2.7.13

When I ran 

`python ice_cnv.py rawdata_100000.matrix --bed-file rawdata_100000_abs.bed`,

it did output a file rawdata_100000.matrix_cnv_iced.matrix

But when I then ran 

`python ice_cnv.py rawdata_100000.matrix --bed-file rawdata_100000_abs.bed --remove-cnv`,

an error occurred:

Traceback (most recent call last):

  File "ice_cnv.py", line 217, in <module>

bias_es = iced.normalization._ca_utils.estimate_block_biases(counts, lengths,

AttributeError: 'module' object has no attribute '_ca_utils'

This happened when it was "Estimating CNV-effects."

I couldn't figure out how to go about this. Could someone suggest what to do?

And correct me if I am wrong, I think the first code is to perform LOIC normalization, and the second code with --remove-cnv is to perform CAIC normalization.

Thanks,

Jenny

[Jiani Yin]

I’ve upgraded the iced package to 0.5.7, but it still gives me the same error. 

When I import iced in python 2.7, it gives a warning: The API of this module is likely to change. Use only for testing purposes. "The API of this module is likely to change. "

I tried iced 0.5.1 and it gives the same messages.

Really don’t know what to do.

Jenny

On Apr 16, 2020, at 12:49 PM, Jiani Yin <yinjian...@gmail.com> wrote:

Hi Nelle,

Hope you are doing well. 

Do you see a problem in the iced version that I was using?

Thanks a lot,

Jenny

On Apr 11, 2020, at 12:19 AM, Jiani Yin <yinjian...@gmail.com> wrote:

Hi Nelle,

Thank you for responding! I am sorry, for some reason, I did not see this email earlier.

It was 0.4.2 that I used.

Thanks,

Jenny

On Apr 7, 2020, at 12:00 AM, Nelle Varoquaux <nelle.v...@gmail.com> wrote:

Hello,

Which version of iced are you using? You can find it out through the following command:

python -c "import iced; print(iced.__version__)"

Many thanks,

Nelle

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[Nelle Varoquaux]

Hi Jiani

Then it was indeed a version problem. This warning is not an error: the method should now work. You can safely ignore the warning : it refers to changes that may occur internally.

Thanks,

Nelle

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[Jiani Yin]

Thank you for your response, Nelle.

I tried it again, and this time it stopped at an earlier step with error:

Traceback (most recent call last):

  File "/u/project/jennybea/scripts/ice_cnv.py", line 193, in <module>

    verbose=100, max_iter=args.max_iter, counts_profile=cnv)

  File "/u/home/j/jennybea/.local/lib/python2.7/site-packages/iced/normalization/__init__.py", line 85, in ICE_normalization

    total_counts = X.sum()

AttributeError: 'NoneType' object has no attribute ‘sum'

Maybe the error occurred because I updated the scipy version during my trouble-shooting. I noticed that many codes in the ice_cnv.py script is not compatible with different versions of the packages. Sorry that I am new to python, and this could be because of my ignorance.

I was using ice_cnv.py downloaded from https://github.com/nservant/cancer-hic-norm/blob/master/CNV_norm/ice_cnv.py. It requires a few packages to be imported: argparse, sys, numpy, scipy, pandas, iced, and from iced import io. I know that iced version should be >= 0.5.1. Could you specify which version the other packages should use? Or will you upgrade them all to the latest version? Also which python version do you suggest? 

Thank you very much,

Jenny

[Jiani Yin]

Hi Nelle,

I updated all python modules to the latest version and ran the CAIC package again. But It has been running for 20 days without result. I don't see any error. 

When I tried LOIC, it only took 2 hours and a file named ID_rawdata_100000.matrixcnv_iced.matrix was successfully generated.

Here are the codes I used:

CAIC

python3 ice_cnv.py ./ID_rawdata_100000.matrix --bed-file ./rawdata_100000_abs.bed --remove-cnv --max_iter 100

LOIC

python3 ice_cnv.py ./ID_rawdata_100000.matrix --bed-file ./rawdata_100000_abs.bed

Do you see any problem in the CAIC codes?

Thank you,

Jenny

Hi Nelle,

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